3VCR - JenaLib

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Title :   CRYSTAL STRUCTURE OF A PUTATIVE KDPG (2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE) ALDOLASE FROM OLEISPIRA ANTARCTICA

Authors :   P. J. Stogios, O. Kagan, R. Di Leo, V. Yim, A. Joachimiak, A. M. Edwards, A. Savchenko, Midwest Center For Structural Genomics (Mcsg)

Date :   04 Jan 12 (Deposition) - 18 Jan 12 (Release) - 07 Aug 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.84

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (3x)
Biol. Unit 2: B  (3x)

Keywords :   Unknown Function, Aldolase Superfamily, Class I Aldolase, Kdpg Aldolase Domain, Alpha/Beta Protein, Tim Beta/Alpha Barrel, Tim Barrel, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Kube, T. N. Chernikova, Y. Al-Ramahi, A. Beloqui, N. Lopez-Cortez, M. E. Guazzaroni, H. J. Heipieper, S. Klages, O. R. Kotsyurbenko, I. Langer, T. Y. Nechitaylo, H. Lunsdorf, M. Fernandez, S. Juarez, S. Ciordia, A. Singer, O. Kagan, O. Egorova, P. Alain Petit, P. Stogios, Y. Kim, A. Tchigvintsev, R. Flick, R. Denaro, M. Genovese, J. P. Albar, O. N. Reva, M. Martinez-Gomariz, H. Tran, M. Ferrer, A. Savchenko, A. F. Yakunin, M. M. Yakimov, O. V. Golyshina, R. Reinhardt, P. N. Golyshin
Genome Sequence And Functional Genomic Analysis Of The Oil-Degrading Bacterium Oleispira Antarctica.
Nat Commun V. 4 2156 2013
PubMed-ID: 23877221 | Reference-DOI: 10.1038/NCOMMS3156

Molecule 1 - PUTATIVE KDPG (2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE) ALDOLASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	P15TV-L
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	OLEISPIRA ANTARCTICA
	Organism Taxid	:	188908

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (3x)	:	A
Biological Unit 2 (3x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
2	PYR	2	Ligand/Ion	PYRUVIC ACID

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
2	PYR	3	Ligand/Ion	PYRUVIC ACID

Biological Unit 2 (2, 12)

No.	Name	Count	Type	Full Name
1	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
2	PYR	3	Ligand/Ion	PYRUVIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:46 , THR A:70 , VAL A:89 , SER A:90 , PRO A:91	BINDING SITE FOR RESIDUE PYR A 301
2	AC2	SOFTWARE	ARG B:46 , THR B:70 , VAL B:89 , SER B:90 , PRO B:91 , THR B:164	BINDING SITE FOR RESIDUE PYR B 301

(no "SS Bond" information available for 3VCR)

Asymmetric Unit

No.	Residues
1	Phe A:138	-	Pro A:139
2	Phe B:138	-	Pro B:139

(no "SAP(SNP)/Variant" information available for 3VCR)

(no "PROSITE Motif" information available for 3VCR)

(no "Exon" information available for 3VCR)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:216
 aligned with D2YW47_OLEAN | D2YW47 from UniProtKB/TrEMBL  Length:217

    Alignment length:216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
         D2YW47_OLEAN     2 MTQLDTWLANTKPLIPVIVIDDLVHAIPMAKALVAGGVHLLEVTLRTEAGLAAISAIKKAVPEAIVGAGTVCTADDFQKAIDAGAQFIVSPGLTPELIEKAKQVKLDGQWQGVFLPGVATASEVMIAAQAGITQLKCFPASAIGGAKLLKAWSGPFPDIQFCPTGGISKDNYKEYLGLPNVICAGGSWLTESKLLIEGDWNEVTRRASEIVKLSDI 217
               SCOP domains d3vcra_ A: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhh...eeee......hhhhhhhhhhh.....eeee.......hhhhhhh......eeehhhhhhhhhhhhhhhhhhhhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vcr A   1 mTQLDTWLANTKPLIPVIVIDDLVHAIPmAKALVAGGVHLLEVTLRTEAGLAAISAIKKAVPEAIVGAGTVCTADDFQKAIDAGAQFIVSPGLTPELIEKAKQVKLDGQWQGVFLPGVATASEVmIAAQAGITQLKCFPASAIGGAKLLKAWSGPFPDIQFCPTGGISKDNYKEYLGLPNVICAGGSWLTESKLLIEGDWNEVTRRASEIVKLSDI 216
                            |       10        20        30        40        50        60        70        80        90       100       110       120    |  130       140       150       160       170       180       190       200       210      
                            |                          29-MSE                                                                                         125-MSE                                                                                       
                            1-MSE

Chain B from PDB  Type:PROTEIN  Length:216
 aligned with D2YW47_OLEAN | D2YW47 from UniProtKB/TrEMBL  Length:217

    Alignment length:216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
         D2YW47_OLEAN     2 MTQLDTWLANTKPLIPVIVIDDLVHAIPMAKALVAGGVHLLEVTLRTEAGLAAISAIKKAVPEAIVGAGTVCTADDFQKAIDAGAQFIVSPGLTPELIEKAKQVKLDGQWQGVFLPGVATASEVMIAAQAGITQLKCFPASAIGGAKLLKAWSGPFPDIQFCPTGGISKDNYKEYLGLPNVICAGGSWLTESKLLIEGDWNEVTRRASEIVKLSDI 217
               SCOP domains d3vcrb_ B: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhh..eeee......hhhhhhhhhhh.....eeee.......hhhhhhh......eeehhhhhhhhhhhhhhhhhhhhhhhh.hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vcr B   1 mTQLDTWLANTKPLIPVIVIDDLVHAIPmAKALVAGGVHLLEVTLRTEAGLAAISAIKKAVPEAIVGAGTVCTADDFQKAIDAGAQFIVSPGLTPELIEKAKQVKLDGQWQGVFLPGVATASEVmIAAQAGITQLKCFPASAIGGAKLLKAWSGPFPDIQFCPTGGISKDNYKEYLGLPNVICAGGSWLTESKLLIEGDWNEVTRRASEIVKLSDI 216
                            |       10        20        30        40        50        60        70        80        90       100       110       120    |  130       140       150       160       170       180       190       200       210      
                            1-MSE                      29-MSE                                                                                         125-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

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)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Aldolase (457)

Family: automated matches (113)

Protein domain: automated matches (113)

Oleispira antarctica [TaxId: 188908] (1)

1a	d3vcra_	A:
1b	d3vcrb_	B:

(no "CATH Domain" information available for 3VCR, only for superseded entry 3LAB replaced by 3VCR)

(no "Pfam Domain" information available for 3VCR)

Asymmetric Unit(hide GO term definitions)

Chain A,B (D2YW47_OLEAN | D2YW47)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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